BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716101.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 2,809,476
number of mapped reads = 2,577,906 (91.76%)
number of supplementary alignments = 9,121 (0.32%)
number of secondary alignments = 0
number of mapped bases = 149,241,965 bp
number of sequenced bases = 149,194,700 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 123,378
duplication rate = 3.41%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.1123
>>>>>>> ACTG content
number of A's = 37,480,635 bp (25.12%)
number of C's = 28,850,043 bp (19.34%)
number of T's = 47,214,396 bp (31.65%)
number of G's = 35,646,691 bp (23.89%)
number of N's = 2,935 bp (0%)
GC percentage = 43.23%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 756,811
number of insertions = 8,849
mapped reads with insertion percentage = 0.34%
number of deletions = 28,871
mapped reads with deletion percentage = 1.11%
homopolymer indels = 44.24%
>>>>>>> Coverage
mean coverageData = 0.0482X
std coverageData = 0.4202X
There is a 4.17% of reference with a coverageData >= 1X
There is a 0.46% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 12517947 0.05022233023844703 0.7013870589860124
chr2 243199373 11749423 0.0483118967580562 0.6207392762445191
chr3 198022430 8602756 0.04344334124169671 0.24045425521627128
chr4 191154276 9294460 0.048622820239710464 0.30303021126825436
chr5 180915260 8547918 0.04724818680303696 0.24623600082570868
chr6 171115067 8014677 0.04683793859017687 0.31504329383860236
chr7 159138663 8450576 0.05310196680488638 0.5907269807095955
chr8 146364022 7920963 0.054118238155548906 0.547326953748133
chr9 141213431 4940460 0.03498576562451768 0.2842753397983697
chr10 135534747 6555771 0.04836967010385905 0.43686387244456387
chr11 135006516 5301870 0.039271215620437165 0.3202164775567496
chr12 133851895 7395452 0.05525100709257796 0.2712601658354367
chr13 115169878 4511604 0.039173472077481925 0.22662497099478696
chr14 107349540 4999135 0.04656876033190268 0.25317094691335956
chr15 102531392 5530956 0.05394402526008815 0.27251740268955016
chr16 90354753 5047033 0.05585796908769149 0.29432087983917105
chr17 81195210 6422191 0.07909568803381382 0.3420799732958346
chr18 78077248 2815432 0.03605957013238991 0.5305629771625072
chr19 59128983 3771602 0.06378601167552636 0.5475399658274275
chr20 63025520 4861442 0.07713450043728318 0.33449673653337225
chr21 48129895 1927782 0.04005373375528868 0.2800421448120599
chr22 51304566 1342603 0.02616926922254834 0.18354503585725224
chrMT 16571 173051 10.443002836280249 6.685755414764632
chrX 155270560 8036445 0.051757686711505387 0.29311688415713055
chrY 59373566 510416 0.008596687623579827 0.3349649622775132